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I understand that flaxseed are a great source of omega-3 fatty acids and should be included in my diet. However they are laxative which I find undesireable. One way to get rid of this effect is to soak them in water over-night to extract the carbohydrates that cause this.

My question is: Does soaking flaxseed over-night deplete them of their oil as well, to any degree worth mentioning, and in that case, how much?

Since oils are not water soluble, I do not think that a significant amount of the oil will be removed by overnight soaking in water. However, since the water is going to enlarge the pores leading into the seed, some oil is bound to escape through them. I would make sure that the soaking is not prolonged in any way to minimize this loss.